The X-Files frequently gives its viewers images that are hard to shake: a demonic death-fetishist skulking through the shadows. An armless and legless inbred woman hidden under a bed. Twin Kathy Griffins. (Okay, forget that last one.) So it's appropriate that "Founders Mutation" opens with an extreme close-up of a heavily bloodshot eye. Someone, it seems, has seen too much.

His name is Dr. Sanjay (Christopher Logan), and he's an employee at Nugenics Technology who, when asked whether his weekend activities were "work or pleasure," responds with a morose, "I haven't known pleasure for quite some time." Life of the party, this one. Things don't get much better for Sanjay when he attends a staff meeting. While the other employees rattle on about their work and their company's mysterious "founder," Sanjay hears a high-pitched screech that nearly doubles him over. As a flock of crows ominously gathers outside, Sanjay catches snippets of his colleagues' conversation reconfigured into commands like "Data is the key" and "Go, now!"

"Can't anyone hear that?!" he screams to blank and perplexed stares before excusing himself. Sanjay then locks himself in a computer-mainframe room, where he starts gathering the "data" he's been psychically ordered to collect. When the screeching becomes too much to bear, he finally and permanently quiets the noise by jabbing the pointy end of a letter opener into his ear canal. What was that again about images you can't shake?

Written and directed by X-Files veteran James Wong, "Founder's Mutation" is an especially strong standalone entry. Wong unapologetically embraces wince-inducing pulp horror, while elegantly dovetailing the episode's narrative with the larger personal story of FBI special agents Fox Mulder (David Duchovny) and Dana Scully (Gillian Anderson), who are called in to investigate. In contrast to the previous episode, "My Struggle," Mulder is now clean-shaven and fitted with a perfectly tailored suit, finally matching Scully in the ready-for-the-cover-of-GQ department. Is it impertinent to ask how such ill-regarded government agents can afford such a killer wardrobe? Eh, just go with it.

A Nugenics lackey, played by Battlestar Galactica's Aaron Douglas, gives the duo the runaround while they investigate the scene of Dr. Sanjay's suicide. So Mulder steals the dead man's cell phone ("You know me, Scully, I'm old school") and uses it to track down "Gupta," one of Sanjay's contacts. Scully helpfully informs her partner that, since Sanjay was from Western India, "Gupta" is likely the Marathi word for "secret." ("I'm old school, Mulder … pre-Google," she quips.)

Here's something else that's old school: Mulder meets Gupta (Vik Sahay) in a Washington bar that — as he quite hilariously discovers — caters to on-the-down-low gay men. When Mulder asks Gupta if they can go somewhere more private, he doesn't realize he's talking in double entendre. The image of Fox Mulder nearly and unwittingly getting fellated in a bar bathroom is pretty damn funny, as is Gupta's scolding insistence that the "repressed" special agent needs to come out of his self-created closet. ("The truth is in here," he says, pointing to a flabbergasted Mulder's heart.)

Thankfully, Wong doesn't just treat it as a joke. Sanjay was Gupta's lover as well as his confidant, and when Mulder tells him that Sanjay is dead, it leads to a lovely and regretful heart-to-heart. With just a few lines, Sahay really makes you feel the crushing weight of losing an intimate. "I just tried to make him feel better," Gupta says. He also directs Mulder to Sanjay's second apartment, where some answers may be found.

Mulder checks in with Scully at the autopsy bay, where she tells him she discovered two words written on the palm of Sanjay's hand: "Founder's Mutation." In one of the episode's most indelible compositions, the duo stands in front of a projected X-ray of Sanjay's skull, the letter opener pierced right into his brain. (It's horrific and humorous all at once.) The plot thickens after the agents visit Sanjay's apartment, where they find photos of children with shocking deformities. Then, Mulder doubles over — he's hearing that same high-pitched screech.

What the heck is going on? Well, if I told you that Melrose Place's Doug Savant was behind it all, would you believe me? It's true, I swear: With nice helpings of menace and arrogance, Savant plays the mysterious "founder," Augustus Goldman, who Mulder and Scully visit after making contact through Our Lady of Sorrows hospital. As Goldman leads them through his facility, the camera pans past a series of locked-off rooms, which house the kids seen in the photographs at Sanjay's apartment. And with that, the episode's mad-scientist vibes come unforgettably to the fore.

The X-Files tends to have incredible makeup effects, and this sequence is no exception: One child is covered in what appear to be dragon scales. Another has oversized arms and hands, which drag along a large piece of paper as he finger paints. Most shocking is the boy stuffing his elephantine face — which looks like it's been melted by a flamethrower — with oatmeal. Almost all of these peripheral characters are onscreen for two seconds tops, but the level of detail in the makeup underscores Goldman's appalling work.

Perhaps, "Founder's Mutation" is best viewed as Wong's reflection and distillation of the show's mythology: The culprit turns out to be a young man named Kyle (Jonathan Whitesell), who is searching for the sister, Molly (Megan Peta Hill), he just recently discovered he had. Kyle and Molly are the children of Goldman, who experimented on them in utero. Those tests gave the siblings extrasensory powers that neither can adequately control, yet ultimately reunite them. Kyle is effectively the Fox Mulder to Molly's Samantha Mulder. And Goldman is the pair's Cigarette Smoking Man.

Try as Mulder and Scully might, their cases can't help but bleed into their lives. The deeper they get into this one, the more the parallels become poignantly apparent. Early on, Mulder is convinced that Goldman is involved with the alien-human hybrid program that was dismantled in the original series, and of which Scully was an unwitting part. At first, he doesn't share his suspicions with Scully, though she quickly intuits the connections. "I'm not a fragile little girl," she says scoldingly to Mulder, before reminiscing about their son William, who was likely created by the hybrid program, and whom she gave up for adoption toward the end of season nine. "Do you ever think about [him]?" she asks. "Yes," Mulder says. "Of course I do. But I feel like I've had to put that behind me."

It's always amazed me how Duchovny and Anderson can take a soapy plot like the William story line and shade it with such profound sense of loss and regret. (Yet another benefit of two performers who have that rare magical spark between them.) Two of the finest scenes in "Founder's Mutation" detail each agent's fantasy of what it would have been like to raise William, played at different ages by child actors Hannah, Aiden, and Rowan Longworth. Scully imagines her son's first day of school, tending to him after he breaks his arm, and finally, watching as he horrifyingly mutates into something akin to Goldman's subjects.

In the episode's powerful closing sequence, we see Mulder's vision. It begins with him and William watching Stanley Kubrick's epochal 2001: A Space Odyssey, and climaxes with William abducted in a manner eerily similar to Mulder's own sister. Before the dream's troubling end, however, there's a lovely scene between Mulder and William in which he offers his son several interpretations of 2001's black monolith. "Some people think it represents our first contact with aliens," he says, "Other people think it represents the beginning of human knowledge." (A father flailing about, trying to satiate his child's natural curiosity.) Then he hits on the quite affecting truth of the matter: "I think one day you'll probably have your own ideas about it."

Musings of a Non-Cigarette-Smoking Fan:

"Founder's Mutation" is the second episode of the mini-series, but it was shot fifth in the production schedule. The show's science adviser, Anne Simon, tweeted that Chris Carter and "all agree [the] story flows better this way." There's precedent for The X-Files airing out of production order, an occasional practice that began in season four, often to accommodate actors' schedules. Still, I wonder if this might be a situation akin to Glen Morgan and James Wong's season four installment "Never Again," in which Scully has an implied one-night stand with a guy whose tattoo is driving him insane. That episode was originally supposed to air before the revelation of Scully's cancer in "Leonard Betts," but because of some post–Super Bowl scheduling, Carter and the Fox suits decided to air it after that plot twist. Scully's behavior was thus given a retroactive justification that Morgan and Wong (and Gillian Anderson, according to her own statements) didn't intend. Similar thing here?

Further to the rejiggered airing order: When Mulder and Scully visit Walter Skinner (Mitch Pileggi), one of the assistant FBI director's lines ("Welcome back, you two") is clearly dubbed. Obviously, this was done to emphasize that "Founder's Mutation" is Mulder and Scully's first case back on the X-Files. But I do wonder: Will any changes need to be made to Glen Morgan's "Home Again" — the original second episode, which is now scheduled to air fourth — to accommodate this?

Mulder quips about both Edward Snowden and Obamacare. That'd probably be more irritating if Duchovny didn't have such an endearingly flip way of tossing off such topical references.

Unmentioned guest actor No. 1: Rebecca Wisocky, who plays Jackie Goldman, the ex-wife of Savant's Augustus Goldman. Mulder and Scully interview her in a mental hospital where she's been confined for killing the unborn Kyle. (Actually, she cut open her womb to let the boy out and fend for himself — quite another unforgettable image, that.) Wisocky is superbly unhinged, and gets the episode's biggest laugh when she throws a piece of fruit at a cat.

Unmentioned guest actor No. 2: Kacey Rohl, formerly Abigail Hobbs on Hannibal, is excellent in her one scene as an unwilling "incubator" for Goldman's experiments.

Unmentioned guest actor No. 3: Amanda Burke as Kyle's adopted mother, Rebecca. Ever since the trailers for this mini-series debuted, I've been waiting to see Burke's character shout, "Get out!" at Mulder and Scully. Imagine my delight when she also got to say the episode's pulpiest line: "Bad things happen when the birds gather."

I have to mention two other bits of dialogue, both of which made me swoon. From Scully: "A mother never forgets," said during the agents' interview with Jackie Goldman. And from Mulder: "You're never just anything to me, Scully," said during their discussion about William. Be still my heart.

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